FIELDimageR pipeline:
Agriculture and plant breeding image analysis on R environment

Introduction

Agriculture and plant breeding

Images can be used in plant phenotyping to draw inference about many traits:

  • Geometric traits (i.e. plant height, leaf area index, lodging, crop canopy cover)
  • Canopy spectral texture (spectral features)
  • Physiological traits (i.e., chlorophyll, biomass, pigment content, photosynthesis)
  • Abiotic/biotic stress indicators (i.e., stomatal conductance, canopy temperature difference, leaf water potential, senescence index)
  • Nutrients (nitrogen concentration, protein content)
  • Yield


FIELDimageR

FIELDimageR is a R package to analyze images and plant phenotyping, and allows to:

  • Crop the image
  • Remove soil effect
  • Build vegetation indices
  • Rotate the image
  • Build the plot shapefile
  • Extract information for each plot
  • Evaluate stand count, canopy percentage, and plant height


FIELDimageR pipeline

1) Example 01

Remote sensing (Potato Breeding)

Jeffrey Endelman and Filipe Matias (UW-Madison)

Data Info (R/FIELDimageR)

  • Potato breeding: 196 plots (3x15 feet)
  • Population: 138 genotypes
  • HTP Platform (Dr. Philip Townsend UM-Madison): Cessna-180 airplane + HySpex VNIR-1800 + HySpex SWIR-384
  • Hyperspectral Data: 474 bands

Making the mask by using the RGB to calculate vegetation indices and to remove the soil



2) Example 02

Evaluating disease damage (Tomato Breeding)

Fernando Piotto and Jéssica Nogueira (ESALQ/USP)

  • Donwload: EX2.zip
  • Pictures of 10 genotypes with Xanthomonas perforans

* Parallel

  • Dataset: Visual Score
  • Horsfall-Barratt scale
  • 4 Evaluators
  • (Download: ‘EX2_Data.txt’)

Reference

Matias, F.I. (2019). FIELDimageR Pipeline (tutorial). https://github.com/filipematias23/FIELDimageR

Matias, F.I.; Caraza-Harter, M.; Endelman, J.B. (2020). FIELDimageR: A R Package to Analyze Orthomosaic Images from Agricultural Field Trials. The Plant Phenome Journal. DOI:10.1002/ppj2.20005

Filipe Matias
Department of Horticulture
University of Wisconsin-Madison

2021-02-16